SMOG 2: A Versatile Software Package for Generating Structure-Based Models. - Jeffrey K. Noel; Mariana Levi; Mohit Raghunathan; Heiko Lammert; Ryan L. Hayes; José N. Onuchic; Paul C. Whitford (PLoS Comput. Biol., 2016)

A magnesium-induced triplex pre-organizes the SAM-II riboswitch. - Susmita Roy; Heiko Lammert; Ryan L. Hayes; Bin Chen; Regan LeBlanc; T. Kwaku Dayie; José N. Onuchic; Karissa Y. Sanbonmatsu (PLoS Comput. Biol., 2017)

CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2. - Xinqiang Ding; Ryan L. Hayes; Jonah Z. Vilseck; Murchtricia K. Charles; Charles L. Brooks III (J. Comput. Aided Mol. Des., 2018)

A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. - Ryan L. Hayes; Charles L. Brooks III (J. Comput. Chem., 2021)

Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization. - Jonah Z. Vilseck; Luis F. Cervantes; Ryan L. Hayes; Charles L. Brooks III (J. Chem. Inf. Model., 2022)